Re: [galaxy-dev] custom java tools.xml : problem with classpath

26 Feb 2015

      Hi Peter,

i wrote the tool_dependencies.xml

    <?xml version="1.0"?>
    <tool_dependency>
         <package name="jvarkit" version="1.0.0">
             <install version="1.0.0">
                 <actions>
                     <action type="set_environment">
                         <environment_variable name="JVARKITDIR"
    action="set_to">$INSTALL_DIR</environment_variable>
                     </action>
                 </actions>
             </install>
             <readme></readme>
         </package>
    </tool_dependency>

and updated vcffilterjs.xml

    <?xml version="1.0"?>
    <tool hidden="false"
    id="com.github.lindenb.jvarkit.tools.vcffilterjs.VCFFilterJS"
    version="1.0.0" name="vcffilterjs">
       <requirements>
           <requirement type="package" version="1.0.0">jvarkit</requirement>
         <requirement type="binary">java</requirement>
       </requirements>

       <command><![CDATA[java -cp
    \$JVARKITDIR/commons-jexl-2.1.1.jar:\$JVARKITDIR/commons-logging-1.1.1.jar:\$JVARKITDIR/htsjdk-1.129.jar:\$JVARKITDIR/snappy-java-1.0.3-rc3.jar:\$JVARKITDIR/vcffilterjs.jar
    com.github.lindenb.jvarkit.tools.vcffilterjs.VCFFilterJS -e
    '${expression}' -o ${output} ${input}  ]]></command>
       <inputs>
             <param format="vcf" name="input" type="data" label="VCF
    input"/>
             <param name="expression" type="text" label="javascript
    expression"/>
         </inputs>
       <outputs>
             <data format="vcf" name="output"/>
         </outputs>
       <stdio>
         <exit_code range="1:"/>
         <exit_code range=":-1"/>
       </stdio>
       <help></help>
    </tool>

I still get an error:

(...)

    :24,289 (31) command is: java -cp 
$JVARKITDIR/commons-jexl-2.1.1.jar:$JVARKITDIR/commons-logging-1.1.1.jar:$JVARKITDIR/htsjdk-1.129.jar:$JVARKITDIR/snappy-java-1.0.3-rc3.jar:$JVARKITDIR/vcffilterjs.jar 
com.github.lindenb.jvarkit.tools.vcffilterjs.VCFFilterJS -e 
'variant!=nullX' -o 
/home/lindenb/tmp/GALAXY/galaxy-galaxy-dist-32e4527bab2d/database/files/000/dataset_27.dat 
/home/lindenb/tmp/GALAXY/galaxy-galaxy-dist-32e4527bab2d/database/files/000/dataset_1.dat; 
return_code=$?; c
(...)
galaxy.jobs DEBUG 2015-02-26 13:31:24,333 (31) Persisting job 
destination (destination id: local:///)
galaxy.jobs.runners.local DEBUG 2015-02-26 13:31:25,689 execution 
finished: 
/home/lindenb/tmp/GALAXY/galaxy-galaxy-dist-32e4527bab2d/database/job_working_directory/000/31/galaxy_31.sh
galaxy.jobs.output_checker INFO 2015-02-26 13:31:25,717 Job 31: Fatal 
error: Exit code 1 ()
galaxy.jobs DEBUG 2015-02-26 13:31:25,784 setting dataset state to ERROR

The error displayed in galaxy is just an empty VCF header (that why I 
asked about the error log)

Thank you for your help

PS: By the way, my argument was -e 'variant!=null;' , why do I see '-e 
'variant!=nullX'  in the log ?

Pierre
...
On Thu, Feb 26, 2015 at 10:59 AM, Pierre Lindenbaum
<pierre.lindenbaum@univ-nantes.fr> wrote:
...
Hi Galaxy,
I'm trying to put one of my java tool in galaxy.
I've copied the required files in my tool directory under /tools/jvarkit (I
can see it galaxy)
$ ls
     commons-jexl-2.1.1.jar
     commons-logging-1.1.1.jar
     htsjdk-1.129.jar
     snappy-java-1.0.3-rc3.jar
     vcffilterjs.jar
     vcffilterjs.xml
Here is the content of vcffilterjs.xml
<?xml version="1.0"?>
       <tool hidden="false"
id="com.github.lindenb.jvarkit.tools.vcffilterjs.VCFFilterJS"
version="1.0.0" name="vcffilterjs">
         <requirements>
           <requirement type="binary">java</requirement>
         </requirements>
         <command><![CDATA[java -cp
$INSTALL_DIR/commons-jexl-2.1.1.jar:$INSTALL_DIR/commons-logging-1.1.1.jar:$INSTALL_DIR/htsjdk-1.129.jar:$INSTALL_DIR/snappy-java-1.0.3-rc3.jar:$INSTALL_DIR/vcffilterjs.jar
com.github.lindenb.jvarkit.tools.vcffilterjs.VCFFilterJS -e '${expression}'
-o ${output} ${input}   2> /tmp/error ]]></command>
         <inputs>
           <param format="vcf" name="input" type="data" label="VCF input"/>
           <param name="expression" type="text" label="javascript
expression"/>
         </inputs>
         <outputs>
           <data format="vcf" name="output"/>
         </outputs>
         <stdio>
           <exit_code range="1:"/>
           <exit_code range=":-1"/>
         </stdio>
         <help>(...)</help>
       </tool>
When I run this tool, the log says:
NotFound: cannot find 'INSTALL_DIR'
If I replace $INSTALL_DIR with \$INSTALL_DIR ,
Yes, you need to escape the dollar sign.
...
the  error on stderr is :
Error: Could not find or load main class
com.github.lindenb.jvarkit.tools.vcffilterjs.VCFFilterJS
How can I make this work ?
Try inserting something like this into the command as a diagnostic:
echo "\$INSTALL_DIR" &&
Where do you define $INSTALL_DIR? Is this environment variable
done at system level, or are you trying to do this within a Galaxy
defined package.
If the later, you need a <requirements type="package" ...> tag,
which cross references a package defined within a
tool_dependencies.xml file. See for example:
https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod
...
Bonus question: is there a way to catch the error file to display it in
galaxy when a process fails ?
Which error file? Do you mean stderr? That is captured and
visible via the "eye" icon when the dataset is expanded in
the history pane.
Peter